A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems

Character coding entails assumptions that may be problematic within the context of parsimony analysis using current computer algorithms. The example discussed here involves a character-variable (e.g., tail color) that is inapplicable in some taxa in the analysis because the part (e.g., tail) with which it is associated is lacking in those taxa. The part and character-variable can be coded as separate characters, or they can be fused into a single character. If the part and character-variable are coded as separate characters there is transformational independence between the part and the character-variable, but the logical dependence inherent to the hierarchical relationship between the part and its character-variable is only partly accounted for. Fusing the part and character-variable into one multistate character fully accounts for the logical dependence, but it is equivocal regarding the transformational independence. Separate coding is consistent with the primary homology statement that the part is homologous in all taxa possessing it, whereas fused coding is equivocal regarding this hypothesis of primary homology. As a result fused coding involves a loss of phylogenetic information. Use of a stepmatrix or other mechanisms associated with fused coding that preserve this phylogenetic information involves weighting schemes or ordered characters that have other assumptions that may also be difficult to justify.     

Some notes on relation between taxon and character in taxonomy (regarding the paper of A.A. Stekol'nikov "A problem of truth...", Zhurnal Obshchei Biologii. 2003.V.64. No 4. P.367-368)

Under brief consideration is the problem of primary or secondary status of the judgments about taxa relative to the judgments about characters in the biological classifications. The following formal definition of taxonomic system (classification) TS is provided: TS = BT[T, C(t), R(t), R(c), R(tc)], where BT is a biological theory constituting content-wise background of the system, T is a set of taxa, C(t) is a set of taxonomic characters, R(t) is a set of relationships among taxa (similarity, kinship, etc.), R(c) is a set of relationships among characters (homology, etc.), and R(tc) is a set of correspondences among taxa and characters. The latter correspondences may be complete or incomplete. At ontological level, there two basical traditions exist in biological systematics regarding R(tc) according to which the biological diversity is patterned either as a set of groups of organisms (taxa) or as a set of their properties (characters). In the first case, taxon is "primary" relative to character (in cladistics); in its opposite, character is "primary" relative to taxon (in scholasticism, classical typology, classical phylogenetics). At epistemological level, incompleteness of the taxon-character correspondence makes classificatory procedure iterative and taxonomic diagnoses context-dependent. The interative nature of classificatory procedure makes the "primary" or "secondary" status of both taxa and characters relative and alternating. This makes it necessary to introduces a kind of uncertainty relation in biological systematics which means impossibility of simultaneous definition of both extensional and intentional parameters of the taxonomic system at each step of classificatory iterations.     

On homology

The currently most widely used definitions of homology, which concentrate exclusively on what I call phylogenetic homology, involve comparisons between taxa. Although they share important conceptual relationships with phylogenetic homology and their role in evolutionary biology is significant, serial and other forms of iterative homology have been, by comparison, overlooked. There is need for a more inclusive definition of homology. I propose that the basis of homology in the broad sense is the sharing of pathways of development, which are controlled by genealogically-related genes. Using this definition, one can construct hierarchies of homology, and recognize different degrees or strengths of homology. Because different aspects of structures are controlled by distinct developmental programs, it is sometimes necessary to speak of homologies of different attributes of specific structures, rather than to homologize the structures per se. For good biological reasons, parallelism may be difficult to distinguish from homology, and one must in practice be willing to tolerate some ambiguity between them. The formulation I present leads to some unorthodox conclusions about homology in mammalian dentitions and homology between the fore-and hindlimbs of tetrapods.     

Hypothetical Ancestors and Rooting in Cladistic Analysis

Most hypothetical ancestors that are used to root trees in cladistic analyses summarize character-state information in one or more outgroup taxa. Nonetheless, hypothetical ancestors also provide a means of rooting trees using the ontogenetic and paleontological methods of polarizing character transformations, and for incorporating the inferences of more than one of these methods into a single analysis. However, the use of one hypothetical ancestor that combines inferences based on outgroup comparison with those based on other methods of polarizing character transformations to root a cladogram is invalid. Inferences regarding plesiomorphic character states based on outgroup comparison apply to the outgroup node, whereas inferences based on either the ontogenetic or paleontological method apply to the ingroup node. These inferences cannot be combined into a single hypothetical construct. A hypothetical ancestor based on outgroup information is included in the data matrix and used to root the resulting network; however, because this ancestor places potentially problematic constraints on the analysis, the use of actual outgroup taxa is preferable in most instances. Correct use of a hypothetical ancestor inferred with the ontogenetic and paleontological methods involves the Lundberg method in which the shortest ingroup network is rooted at the internode to which the hypothetical ancestor attaches most parsimoniously. Because inferences of polarity based on outgroup comparison cannot be combined directly with those based on other polarization methods, the synthesis of information from all three methods in a single tree must involve taxonomic congruence.     

Parallel tion in the context of character analysis

For the establishment of polarity of character transformation prior to phylogenetic analysis, various logical and biological criteria are discussed; some are rejected on grounds of liability to systematic error, circularity or unwarranted assumptions aboutParallel tion is used as a non-polar term, with forward and reverse to indicate polarity. A computer program for the detection of parallel tion is described which takes taxa in groups of four. The characters, with two derived: two primitive states or three derived: one primitive state, are listed according to the distribution of states over the four taxa. To each of the 15 phylogenies there corresponds a compatible pair of character patterns. Discordant 2: 2 patterns are unconditionally incompatible (Le Quesne test failure), discordant 3: 1 patterns are incompatible conditional upon correct scoring of polarity. For any putative phylogeny the concordant and discordant characters are identified. In cases of competing alternatives these character sets have to be weighed against one another. Character weighting is discussed; it is argued that it is the individual character transformation which should be weighted, in each direction separately.     

Morphometrics and character state recognition for cladistic analyses in theBletia reflexa complex (Orchidaceae)

Different criteria have been suggested for decisions on character state recognition for morphological characters showing continuous variation from taxon to taxon. A method proposed byMishler andDe Luna seeks to recognize as many character states as the groups of taxon means that are revealed by an analysis of variance (ANOVA) followed by multiple range tests. We apply this method as a guide in decisions of selecting taxonomic characters in species of theBletia reflexa complex. Seven species of the complex, represented by 156 individuals belonging to 54 populations, were the terminal taxa of the study. Character state codes were assigned to 20 characters. These characters together with 12 non-quantitative characters were incorporated into cladistic analyses. Results indicate that the complex is monophyletic only under one outgroup combination.     

Taxon sampling, character sampling and systematics: how gradist presuppositions created additional ganglia in gastropod euthyneuran taxa

In gastropods, the pentaganglionate condition of the nervous visceral loop has been accepted as a general character and one of the most important synapomorphies of the Euthyneura. The review of published data on 50 generic taxa shows an extreme confusion in both terminology and application of the homology concept to the two parietal ganglia observed in some Euthyneura, in addition to the three observed in most gastropods. A parsimonious re-interpretation of the data leads to the conclusion that the occurrence of five visceral ganglia is ascertained in only six genus-group taxa, and therefore cannot be accepted as a general character of Euthyneura. We propose that in phylogenetic analysis, taxonomic sampling should be determined according to the variability of characters and independently of the rank of the taxa taken into account, until every taxon in the data matrix is monomorphic for every character, and until all the taxa in which the characters occur are represented in the data matrix. We propose to use the term 'domain of definition' of a character for such a taxonomic sample. Implementing the domain of definition of characters in construction of data matrices would avoid the abuse of generalities leading to circularity in evolutionary interpretations of classification, which in the case of Euthyneura result from an a priori gradist interpretation of the evolution of the nervous system.     

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study

Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.     

The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations

As the basis for comparative biology, correctly assigning character homology is critical. Yet, identifying homologous characters in practice is often challenging. Among the major roadblocks is that the mechanistic bases of character homology remain in question. Thus, investigators must rely on several independent lines of evidence (e.g., character anatomy, phylogenetic distribution, or embryological position); however, these distinct sources of evidence often lead to conflicting diagnoses of character homology. What is more, there is no consensus regarding the relative importance of distinct lines of evidence for determining character homology. Here, we review the difficulties that have hindered the search for the mechanistic bases of character identity, and relate these issues to a recently proposed mechanistic hypothesis of character identity--the Character Identity Network Hypothesis. Next, using two well-studied cases of homology conflict (i.e., avian and skink digit identity), we assess the utility of different lines of evidence in diagnosing homology. We conclude that, when comparing adult structures, because anatomical characters more closely reflect the actions of the developmental genetic mechanisms of character individuation they are more reliable than embryological homology criteria.     

Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty

Data on fossil taxa can, and should, be incorporated into cladistic analyses. Potential problems with such analyses include large amounts of missing data, and uncertainty about homology of parts that are present. Ambiguity of character data may also occur with extant taxa, but rarely to the extent that it occurs in fossil data. Such ambiguity reduces the strength of the test of character congruence among taxa, in effect relaxing the criterion of parsimony. In order to minimize such effects, composite fossil taxa should be avoided when possible, and polymorphisms reduced by breaking terminals into monomorphic subunits. When results including fossils differ radically from those that exclude fossils, such differences should be approached with caution, keeping in mind the reduced strength of the parsimony analysis when large numbers of cells in a matrix are scored as ambiguous. At this point, there is no simple way to compare the “strength” of parsimony between two data sets that have different numbers of characters and/or taxa in relation to missing data. However, methods under development may provide ways to incorporate the effect of missing values into relative measures of group support such as Bremer support, character removal, and the bootstrap.     

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.     

Investigation of serological determinants from single storage plant proteins

The main storage proteins of the angiosperms provide valuable characters for taxonomic research. By comparing the reactivity of one specific protein in different taxa (mainly Ranunculaceae). determinants or determinant groups can be discriminated. Their number is a function of the number of the reference or anti-systems and of the number of taxa compared. These serological determinants prove a posteriori to be good characters and most useful in taxonomy. Their systematic range extends from one genus to the whole of the angiosperms. The resolving power is best between genera within a family. Using such a single protein system, it is possible to co-ordinate the determinants of the taxa investigated and to map their distribution; this is an advantage over the multi-protein systems commonly used. By serological comparison, it should be possible to establish the homology of the main storage globulins throughout the angiosperms.     

Homologies in phylogenetic analyses—concept and tests

Analyzing morphological characters in a phylogenetic context comprises two steps, character analysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on homology. The concept of homology concerns comparable parts of the same or different organisms if their correspondences are the consequence of the same genetic or epigenetic information, and consequently of the same origin. The concept of homology is more inclusive than the character concept. Characters are seen as parts of transformation series. In the first step of morphological character analyses correspondences and non-correspondences between two characters are analyzed. A range of different examination methods and accurate study contribute to the severity of test. The hypothesis that two characters are homologous is corroborated if the correspondences outweigh the non-correspondences because the non-correspondences contradict the homology hypothesis whereas the correspondences contradict the analogy hypothesis. Complex characters possess a higher empirical content than less complex characters because they are more severely testable. The cladistic analysis tests characters against other characters which have all passed the first test. Characters which are congruent with the most parsimonious topology are further corroborated; incongruent characters are not seen as ‘falsified’ but as not further corroborated and subject to re-analysis. To test both homologies and topologies repeatedly is consistent with Popperian testability, and it is in such cycles of research that hypotheses will be critically re-evaluated.     

QUANTITATIVE CHARACTERS IN PHYLOGENETIC ANALYSIS

Abstract— When analysing phylogcnetic relationships at low laxonomic levels it is often the ease that many of the features that can be used to separate taxa show continuous variation. The theoretical and practical problems for the use of such quantitative characters in phylogenetic analysis arc examined. Three methods of coding continuous data into discrete characters are assessed in detail: simple gap-coding, generalised gap-coding and segment-coding, a form of range-coding. The methods are applied to a data set gathered for Eucatyptus L'Hérit. informal subgenus Symphyomyrtus section Maidenana (Myrtaceae). Each method is capable of distorting relative differences between taxa, but segment-coding produces the least amount of distortion, provided the range of variation of the character is divided into a sufficient number of character states.
Continuous quantitative characters provide data for phylogenetic analysis that arc more noisy than those provided by discrete qualitative characters and should, therefore, only be used when the number of qualitative characters is insufficient for resolution of relationships. The results of such analyses should be recognised as provisional pending the discovery of more readily informative characters.     

The tracheid-vessel element transition in angiosperms involves multiple independent features: cladistic consequences

Current definitions of tracheids and vessel elements are overly simple. These definitions are based on light microscope studies and have not incorporated information gained with scanning electron microscopy (SEM) or transmission electron microscopy (TEM). Current definitions are based primarily on angiosperms, especially eudicots, and were devised before many basal angiosperms were carefully studied. When all sources of information are taken into account, one can recognize changes in six characters in the evolution of tracheids into vessel elements in angiosperms (or vice versa) as well as in other groups of vascular plants. There is an appreciable number of taxa in which all criteria for vessel origin are not met, and thus incipient vessels are present. At the very least, vessel presence or absence should not be treated as a single binary character state change in construction of cladistic matrices. Increase in conductive area of an end wall by means of lysis of progressively greater areas of pit membrane and increase in pit area on the end wall (as compared to pit area on equivalent portions of lateral walls) are considered the most important usable criteria for recognizing intermediacy between tracheids and vessel elements. Primitive character states in vessel elements are briefly discussed to differentiate them from changes in character states that can be regarded as intermediate between tracheids and vessel elements.     

Exhaustion of morphologic character states among fossil taxa

Frequencies of new character state derivations are analyzed for 56 fossil taxa. The hypothesis that new character states are added continuously throughout clade history can be rejected for 48 of these clades. Two alternative explanations are considered: finite states and ordered states. The former hypothesizes a limited number of states available to each character and is tested using rarefaction equations. The latter hypothesizes that there are limited possible descendant morphologies for any state, even if the character has infinite potential states. This is tested using power functions. The finite states hypothesis explains states: steps relationships significantly better than does the ordered states hypothesis in 14 cases; the converse is true for 14 other cases. Under either hypothesis, trilobite clades show appreciably more homoplasty after the same numbers of steps than do molluscs, echinoderms, or vertebrates. The prevalence of the exhaustion pattern among different taxonomic groups implies that worker biases are not to blame and instead implicates biological explanations such as intrinsic constraints or persistent selective trends. Regardless of the source of increased homoplasy, clades appear to exhaust their available character spaces. Nearly all examined taxa show significant increases in proportions of incompatible character pairs (i.e., those necessarily implying homoplasy) as progressively younger taxa are added to character matrices. Thus, a deterioration of hierarchical structure accompanies character state exhaustion. Exhaustion has several implications: (1) the basic premise of cladistic analyses (i.e., that maximum congruence reflects homology rather than homoplasy) becomes increasingly less sound as clades age; (2) sampling high proportions of taxa probably is needed for congruence to discern homoplasy from homology; (3) stratigraphic data might be necessary to discern congruent homoplasy from congruent homology; and (4) in many cases, character states appear to have evolved in ordered patterns.     

Fifty years of character compatibility concepts at work

In the mid 19th century,systematic biologists realized that observable similarities and differences among a group of related species could be the basis for hypotheses about the evolutionary relationships among the species and their ancestors.Such hypotheses Can be expressed as characters.A character is comprised of two or more character states of species considered to be similar with respect to a basis for comparison.The states of a character may also be arranged into a character state tree to hypothesize speciation events associated with changes from one character state to another.In the mid 20th century.some systematists realized that sometimes paxrs of characters(or character state trees)could be incompatible as hypotheses,i.e.,they could not both be true.Through the 1950s,'60s and'70s,tests for,and ways to resolve,incompatibilities were used to estimate an ancestor relation based on mutually compatible characters.An estimate was often shown as a diagram connecting ancestors to their immediate descendants(not quite correctly)called a phylogenetic tree.More recently,other applications of compatibility concepts have been developed,including:identify characters that appear to be random in the context of their data set;combine estimates of ancestor relations for subsets of taxa in a larger collection into a single estimate(a so-called supertree)for the whole collection;and interpret geographic patterns in an evolutionary context.